personally, I used the two case fans as intake on the front fan mounts. I used a h80 with a nh p14 exhausting out the rear fan mount. That met my cooling requirements and the only thing i could hear was the gtx 660 ti and it wasn't very loud at that.

if i had to add something, I would only mount an intake fan in the bottom slot. that way, none of the moduvents are removed. I say this in the interest of keeping the case quiet (because that's what i paid good money for).

vertical cooling is technically more effective, but i would say negligibly so. the R4 is hardly a small case where this would be much more important.